De Novo Assembly from Oligos
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5 weeks ago
Kenneth • 0

Hello,

I am trying to assemble a pseudo-chromosome from a few thousand 130bp oligos with 30bp of overlap. I've aligned all of my reads to their reference and I have at least 20X coverage for each oligo. I've tried megahit and spades but I am not quite getting the correct scaffold. Is there an assembler that is more adept at this style of assembly?

If not, is there a tool that can generate consensus reads from NGS data?

Thanks.

assembly denovo • 136 views
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Perhaps tadpole.sh from BBMap suite may work.

Tadpole guide is available.

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SPAdes should work in this case, so there's either something wrong with your data, or you're using them wrong. Please provide the SPAdes/MEGAHIT commands you ran and explain what you mean exactly by "I am not quite getting the correct scaffold".